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50 lines
1.3 KiB
Python
50 lines
1.3 KiB
Python
#!/usr/bin/env python
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import sys
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from Numeric import *
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from rpy import *
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def fail( message ):
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print >> sys.stderr, message
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return -1
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def main():
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in_fname = sys.argv[1]
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out_fname = sys.argv[2]
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columns = int( sys.argv[3] ) - 1, int( sys.argv[4] ) - 1
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title = sys.argv[5]
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xlab = sys.argv[6]
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ylab = sys.argv[7]
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matrix = []
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for i, line in enumerate( open( sys.argv[1] ) ):
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# Skip comments
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if line.startswith( '#' ):
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continue
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# Extract values and convert to floats
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row = []
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for column in columns:
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fields = line.split( "\t" )
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if len( fields ) <= column:
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return fail( "No column %d on line %d" % ( column+1, i ) )
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val = fields[column]
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if val.lower() == "na":
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row.append( float( "nan" ) )
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else:
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try:
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row.append( float( fields[column] ) )
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except ValueError:
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return fail( "Value '%s' in column %d on line %d is not numeric" % ( fields[column], column+1, i ) )
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matrix.append( row )
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r.pdf( out_fname, 8, 8 )
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r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
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r.dev_off()
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r.quit( save="no" )
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if __name__ == "__main__":
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main()
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